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Expressed SSRs (G. herbaceum)

 
  Drought transcriptomic sequences of five cDNA libraries of G. herbaceum were explored to develop SSRs markers. Out of all the unigenes (contig and singletons), resulted in the assembly of the transcriptome sequencing, a total of 99,780 unigenes (having more than 180 bp) were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs (eSSRs).
  All the expressed SSRs have been submitted to NCBI GenBank under GenBank accession numbers: ...............  
 
Summary statistics of screening of transcriptome of cotton (G. herbaceum) for expressed SSRs  
Summary of Screening/sequencing
Total Number of reads in trancriptome sequencing 318872
Number of unigenes after assembly 147510 (40550 contigs and  106960 singletons)
Number of transcripts analyzed with greater than 180 bp 99780
Number of SSR containing sequences               8900 (containing 12471 SSRs)
Number of sequences containing more than 1 SSR 1948
Number of SSR contining sequences used for primer designing 3299 (containing 4311 SSRs)
Number of SSR contining sequences unsuitable for primer designing 5601 (containing 8160 SSRs)   
Number of SSR contining sequences used for primer synthesis 100
Average size of the contigs 0.3Kb
Estimated transcriptome screened
(number of contigs analyzed x. average contigs size) 
29.9Mb    

 

     
                 Frequency deatils of G.herbaceum expressed SSRs repeat motifs